Ebola puzzle 1000
We've been quiet about Ebola for a while. I just wanted to let folks know that we have gone over the results from Puzzle 1000, and players have produced some very promising starting points for design. In particular, the top-scoring solution, which came from the GoScience team, has a couple of hydrophobic amino acid residues providing very nice shape-complementarity to the binding pocket, and also happens to form a nice beta-hairpin (with a couple of good backbone hydrogen-bonds) that can serve as a great starting point for further design. The GoScience design is shown in purple in the cross-section below, with the Ebola glycoprotein in green.
The second-place team, the Contenders, also filled the pocket quite well, using two aliphatic amino acid side-chains rather than an aliphatic and an aromatic. This also was in a hairpin conformation. The fact that players were hitting on a consistent backbone conformation over and over also helps us: it tells us that this is the backbone conformation that tends to fit here, narrowing our search.
There were a number of other interesting designs, too, even though some weren't the top-scoring. L'Alliance Francophone, for example, created a good design that filled the cavity well while simultaneously forming some good hydrogen bonds between the target and the peptide. Please continue to share your most interesting designs with the scientists, whether or not they're the top-scoring!( Posted by v_mulligan 80 2317 | Thu, 01/15/2015 - 21:49 | 6 comments )
New IRC Server!
Today we're deploying something that we've been working on behind the scenes recently - the new IRC server!
Our old IRC server was using unsupported and unmaintained software, which made it difficult to update when we needed new features or bug fixes.
You likely wont see much of a change with the new server, but here are a few things that will be different:
* If you want to connect to the new server with your own IRC client, you will need to connect to port 6665 instead of port 6667 on irc.fold.it (We may switch this to the default 6667 at a later date).
* If you're using your own IRC client, you will need to repeat the process of configuring it to identify on the new server (adding your IRC key). You may have added your IRC key for the old server, but this is a new server, so you'll have to do it again.
* You will now only be able to join #global, #veteran, and your group channel.
* Group admins will automatically have oper privileges in their own groups (the group leader is able to flag who is and who isn't admin on the website).
* The server wont automatically ban you if you fail to identify before joining your group channel. As long as you identify, you should be able to rejoin immediately.
* The upgrades include an additional feature for downloading old puzzles. You can now download old puzzles just like you download recipes off the site. You need to be logged into chat in your Foldit client, and also logged into the website. When you are, there is a link on the Puzzle page, immediately above the comments section. Clicking that link will download the puzzle. (This will be enabled soon). Note that we don't officially support old puzzles, but if the puzzle is fairly recent, it should still work!
* The server and chat should be more reliable overall, barring some initial kinks that may have to be worked out.
What wont change:
* Behavior while using the Foldit client chat.
* You'll still IDENTIFY with NickServ as usual when using your own IRC client.
* You can still join #global and #veteran without identifying.
Any new clients that start up will connect to this server automatically, but you'll have to restart your old clients. It may take a while for everyone to restart and migrate to the new server.
Some of our players have already helped to test the new server, but there might be some bugs that we haven't found yet. Feel free to respond to this post if you notice anything that isn't working properly!( Posted by jflat06 80 669 | Tue, 01/13/2015 - 19:55 | 5 comments )
Through the eyes of a scientist - Puzzle 1018
Baker Lab scientist bkoep recently sat down with Foldit players' designs from Puzzle 1018 for a visual inspection, which is the first step in our analysis of Foldit designs. Join us as we take a critical look at the latest symmetric proteins designed by Foldit players and voice some thoughts about the really cool things Foldit players are demonstrating in protein design!
In the video, you'll also hear brief discussion on the following topics:
- hydrogen bond networks
- core packing
- hydrophobic interfaces
- special considerations when designing with GLY, CYS, and MET residues
We apologize for the inconsistent sound quality—subtitles can be accessed on YouTube with the "CC" button below the video frame.
Check it out and leave your questions in the comments below!( Posted by bkoep 80 1005 | Tue, 12/16/2014 - 00:56 | 14 comments )
Help us to solve a Vascular endothelial growth factor protein!
Vascular endothelial growth factor (VEGF) is a protein released to trigger new blood vessels to form. This is important in embryonic development and when healing from cuts and damage, but it can also be hijacked by cancer cells to trick the body into providing extra blood vessels (angiogenesis).
Puzzle 1012 comes from the VEGF receptor (type 1). The receptor forms a membrane dimer, with an extracellular part that binds VEGF and an intracellular kinase domain which is responsible for signaling. The extracellular portion consists of seven Immunoglobulin-like (Ig) domains. This puzzle consists of the sequence for domain 6.
Some experimental data has been collected for the VEGF receptor, but it hasn't yet lead to a finished structure. The hope is that if you can help us find near-native solutions then your Foldit predictions can be used to improve the structure. That in turn could lead to a better understanding of angiogenesis and eventually to new anti-cancer treatments.
Please try out the first puzzle for this unsolved protein here .
UPDATE: try out the second puzzle for this unsolved protein here .( Posted by beta_helix 80 2317 | Wed, 11/12/2014 - 20:18 | 1 comment )
Exploit found in puzzle 1000
A few players have pointed out a small problem in puzzle 1000 that can be exploited to get a few extra points: if the non-designable residues at the start and end of the peptide are deleted, and then reinserted, they become designable, meaning that you can now design five positions instead of the intended three. We don't think that this will invalidate the scientific results from this puzzle, so rather than re-post it, we are announcing the exploit so that no one has an unfair advantage. Feel free to design all five positions using this exploit.( Posted by v_mulligan 80 2317 | Thu, 10/23/2014 - 00:39 | 0 comments )